Alignments for a candidate for thrC in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Desulfovibrio vulgaris Hildenborough

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate 208732 threonine synthase

Query= reanno::Miya:8501211
         (492 letters)



>MicrobesOnline__882:208732
          Length = 482

 Score =  798 bits (2062), Expect = 0.0
 Identities = 387/482 (80%), Positives = 429/482 (89%), Gaps = 1/482 (0%)

Query: 10  PGHDFPTARTRMEYVCLGCGERRGIDELLYTCPSCGGVYLLEDLDFDTLAEQRTGPEWRA 69
           P  DFP  R+RMEYVCLGCG R  IDELLYTCPSCGGV+LLEDLDFD LA+ R+G +WR 
Sbjct: 2   PSCDFPGWRSRMEYVCLGCGARHSIDELLYTCPSCGGVFLLEDLDFDHLADHRSGDDWRT 61

Query: 70  LFDARAATRTTALRGIFRFYELMAPVLEEEDIVYLGEGNTPIVEAAPVLRDAVGIPFAFK 129
           LFD+RA+TR  +LRGIFRFYELMAPVLEE+DI+YLGEGNTP+V+A+P L  +VG  FA+K
Sbjct: 62  LFDSRASTRCRSLRGIFRFYELMAPVLEEDDIIYLGEGNTPVVDASPALERSVGQRFAYK 121

Query: 130 NDGQNPSASFKDRGMACAFSYLKALVRKHGWDEVLTVCASTGDTSAAAALYASYVGGPVK 189
           NDGQNPSASFKDRGMACAFSYL+ALVRKHGWDEVLT+CASTGDTSAAAALYASYVG P+K
Sbjct: 122 NDGQNPSASFKDRGMACAFSYLRALVRKHGWDEVLTICASTGDTSAAAALYASYVGSPIK 181

Query: 190 SVVLLPHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALLNSKNSWRIL 249
           S V+LPHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALLNSKNSWRIL
Sbjct: 182 SAVILPHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALLNSKNSWRIL 241

Query: 250 GQESYAFEVAQWYGWDMKGQCVFVPIGNAGNVTAIMAGFLKLLRLGVIDALPRVIGVQSH 309
           GQESYAFEVAQWYGWDM G+CVFVPIGNAGN+TA+M+GFLK+ RLG+IDALPRV GVQSH
Sbjct: 242 GQESYAFEVAQWYGWDMAGKCVFVPIGNAGNITAVMSGFLKMHRLGIIDALPRVFGVQSH 301

Query: 310 HADPVWRYYSQPDPATRTYAPVTVQPSVAQAAMIGNPVSFPRVKALADRFIAEGGERAFS 369
           HADPV+RYYS  DP  R Y PVTVQPSVAQAAMIGNPVSFPRV+ LA+RF A GG  AF 
Sbjct: 302 HADPVYRYYSVEDPRQRHYEPVTVQPSVAQAAMIGNPVSFPRVRHLAERFEALGGPGAFQ 361

Query: 370 VVQVTEQEIMDAMIRGNRHGHIACTQGGECLAGLIKARELGLVSQGEHAVLDATAHSLKF 429
           VVQVTEQ IMD+MIR NRHGHIACTQGGECLAGL++A+ELGLV + E AVLDATAHSLKF
Sbjct: 362 VVQVTEQAIMDSMIRANRHGHIACTQGGECLAGLLRAKELGLVDKDETAVLDATAHSLKF 421

Query: 430 AGFQDMYFTNSFPPEYGVTPDASLANAPALVVSPEDKARLSPEAYTLAAAKAVVARLGLA 489
           +GFQDMYFTN FPP YGVTPDA+L NAP+LV+  EDK  L+ E YT+ AA+ + A+LGLA
Sbjct: 422 SGFQDMYFTNGFPPAYGVTPDATLGNAPSLVLHDEDKVALA-EKYTVEAAQRIAAKLGLA 480

Query: 490 KK 491
            K
Sbjct: 481 GK 482


Lambda     K      H
   0.320    0.136    0.416 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 821
Number of extensions: 33
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 492
Length of database: 482
Length adjustment: 34
Effective length of query: 458
Effective length of database: 448
Effective search space:   205184
Effective search space used:   205184
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate 208732 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00260.hmm
# target sequence database:        /tmp/gapView.25126.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00260  [M=340]
Accession:   TIGR00260
Description: thrC: threonine synthase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    1.5e-57  181.3   0.0    1.9e-57  180.9   0.0    1.1  1  lcl|MicrobesOnline__882:208732  threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:208732  threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.9   0.0   1.9e-57   1.9e-57       4     336 ..      81     419 ..      77     423 .. 0.84

  Alignments for each domain:
  == domain 1  score: 180.9 bits;  conditional E-value: 1.9e-57
                       TIGR00260   4 yreilevt.ekdlvdlaegstelfr.spklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne...... 74 
                                     y+ + +v  e d++ l eg+t++++ sp+l++ vg+ +   k+++ +P+ +FKDrg   +a ++++++ l ++      
  lcl|MicrobesOnline__882:208732  81 YELMAPVLeEDDIIYLGEGNTPVVDaSPALERSVGQ-RFAYKNDGQNPSASFKDRG---MACAFSYLRALVRKhgwdev 155
                                     56667788899*************835889999999.*******************...********999988899999 PP

                       TIGR00260  75 tvlcAtsGdtgaaaa.ealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedkeklkl 152
                                     + +cA++Gdt+aaaa +a +  + +k  v++P+gk+    ++l + l ++a+vl+i G FDd+ ++v++++e+ + ++l
  lcl|MicrobesOnline__882:208732 156 LTICASTGDTSAAAAlYASYVGSPIKSAVILPHGKVT--PQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALL 232
                                     999*******99876366666777999**********..9*******************************98888888 PP

                       TIGR00260 153 nsvNsinparieaqktyafeiveqlgk.espdkvvvpvp.sgnfgailkGflekkelg....lpieklaiaaegaadiv 225
                                     ns N     ri++q +yafe+++ +g+  + + v vp++ +gn++a++ Gfl++++lg    lp +  ++++  a +++
  lcl|MicrobesOnline__882:208732 233 NSKN---SWRILGQESYAFEVAQWYGWdMAGKCVFVPIGnAGNITAVMSGFLKMHRLGiidaLP-RVFGVQSHHADPVY 307
                                     8888...66******************556677999****************************.*************9 PP

                       TIGR00260 226 rrflksg....dlepkedkeTlstAmdignpsnveralelarrslgnledlke...svsdeeileaikklaeeegylle 297
                                     r +  +     + ep + +  +++A  ignp++++r+ +la+r  + +        +v++++i++ +   a+++g ++ 
  lcl|MicrobesOnline__882:208732 308 RYYSVEDprqrHYEPVTVQPSVAQAAMIGNPVSFPRVRHLAERFEALGGPGAFqvvQVTEQAIMDSM-IRANRHGHIAC 385
                                     988644311214555555588999999************9999876654322122266766666655.55666666677 PP

                       TIGR00260 298 phtavavaalkklvekgvsatadpaKFeevvealtgnkl 336
                                     + ++  +a+l++  e g    +d++  e++v+  t ++l
  lcl|MicrobesOnline__882:208732 386 TQGGECLAGLLRAKELG---LVDKD--ETAVLDATAHSL 419
                                     8999*********9999...77777..777775555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (482 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 13.37
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis